Structure of PDB 8cxx Chain B Binding Site BS01

Receptor Information

>8cxx Chain B (length=550) Species: 272563 (Clostridioides difficile 630)

GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

Ligand information

>8cxx Chain F (length=14)

ttcaaaaagtccca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cxx Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
• Resolution: 2.34 Å
• Binding residue (original residue number in PDB): Y30 N165 Y168 H171 K173 K193 Y221 S227 F253 I256 G257 Q346 R432 W439 R441 K456 Y476 K511 M513 S514 Y521 N523
• Binding residue (residue number reindexed from 1): Y3 N138 Y141 H144 K146 K166 Y194 S200 F226 I229 G230 Q319 R405 W412 R414 K429 Y449 K484 M486 S487 Y494 N496

Enzymatic activity

• Enzyme Commision number: 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008168 methyltransferase activity
• GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity

Biological Process

• GO:0006304 DNA modification
• GO:0032259 methylation

External links

• PDB: RCSB:8cxx, PDBe:8cxx, PDBj:8cxx
• PDBsum: 8cxx
• PubMed: 36581322
• UniProt: Q183J3